#!/bin/bash
set -e

# while getopts  ":s:p:" opts
# do
        # case  $opts  in
        # s)
		# barcode=$OPTARG
		# sample_name=$OPTARG
		
		# ;;
		# p)
		# out_prefix=$OPTARG
		
		# ;;
        # esac
# done
# shift $(($OPTIND - 1))



if [ -z "$2" ]; then
	echo `basename $0` "<input.vcf> <out.txt>"
	exit 1
fi


#-----------------------------------------------
. /mnt/ilustre/app/medical/tools/.var #---------
#-----------------------------------------------

# echo
# echo extractField $1 ANN[*].TRID
# java -Xmx$java_memory -jar $snpsift extractField $1 "ANN[0].TRID" > $2

echo
echo extractField $1 CSQ
java -jar $snpsift extractField $1 CSQ > $2

